Clustal
W (and MUSCLE) are free 'academically developed' software that performs multiple
sequence alignments on DNA and Protein Sequences. You may also be familiar with
ClustalX - A Graphical User Interface to the ClustalW software.

In DNADynamo's
'paged' display output, annotations are displayed and can be added to the sequence
alignments, integrating BLASTs, genbank annotations, user defined annotations
and annotated clustalw /muscle multiple alignments. Coloured and annotated alignments
can be printed to pdf for publication or further import and modification in dedicated
illustration software.

DNADynamo
also provides a 'linear' alignment editor which supports mouse drag editing, making
it easy to manually correct alignments generated by clustalw/muscle, or generate
a complete 'hand made' alignment. When this editor is loaded with a DNA alignment,
you can display a correspondingly translated protein alignment, similar to the
functionality provided by SE-AL software. Using these functions it is possible
to align the DNA sequences with respect to their protein translation, rather than
just to the DNA sequence itself, which some researchers believe generates a more
meaningful alignment for input into phylogenetic tree software. With respect to
this, DNADynamo will also takes a bunch of DNA sequences, translate them, generate
a protein alignment, and then re-assemble a DNA alignment based on the protein
alignment, which takes much of the work out of generating such translation respecting
DNA alignments. The alignments can be output as FASTA files or NEXUS files for
input into phylogenetic software.

example alignment in DNADynamo's 'paged' display which includes annotated
sequences. A linear alignment editor that supports mouse drag editing and simultaneous
dna->protein alignments is also provided